Distribution of DBDs in the TF Regulatory Network
+
+
_
+
_
_
_
metR
_
marA
rhaS
marR
+
fadR
iciA
_
iclR
uidR
metJ
_
_
dnaA
_
rhaR
uxuR
soxS
rob
exuR
lrp
_
soxR
mlc
+
+
yiaJ
malT
melR
araC
nagC
+
malI
glpR
glnG
fecI
+
+
_
+
+
_
fucR
+
+
+
+
gutM
fur
srlR
_
+
_
adiY
rcsB
+
ompR
csdG
+
_
+
hns
_
caiF
tdcA
_
mtlR
arcA
+
betI
lctR
pdhR
galR
tdcR
fnr
Gene Product
galS
_
lysR
“winged helix” DNA
binding domain
_
fis
himA
Homeodomain-like
CRP
fruR
narL
_
cspA
_
Met repressor-like
Nucleic acid-binding
proteins
Negative regulation
with binding site data
appY
Putative DNA-binding
domain
C-terminal effector domain of the
Bipartite response regulator
IHF like DNA-binding domain
Lambda repressor-like DNA binding
domain
Positive regulation
with binding site data
_
Negative regulation
without binding site data
+
FIS-like
Positive regulation
without binding site data
Transcription Factors
and their regulated TFs
Transcription Factors
and their regulated genes
A relatively
complex topology
exists in a simple
organism
The TF network
has four major
regulatory
hubs
which are also
global regulators
in their respective
functional class.
Information on the regulated gene is available for 113 TFs
from RegulonDB. We classified the 113 TFs in to nine
functional classes according to what they respond to and
what they regulate. Each of these functional classes have
one to three proteins (global regulators) that regulate over
50 genes and the other proteins (fine tuners) control fewer
than 20 genes
Number of Examples
18
16
14
12
10
8
6
4
2
0
X=1
X=2
X=3
X=4
X = 17
Number of different TF genes (X)
regulated by a transcription factor
Very few TFs regulate more than one TF
Network Growth by Gene Duplication
Duplication growth models
Model-1: Duplication
of regulated gene
Gene regulatory network in E. coli
Model-2: Duplication
of transcription factor
Model-1
Model-2
32 TFs (out of 110) share regulated genes with
a homologue
197 RG (out of 340) share transcription factors
with a homologue
400 out of the 1233 (~1/3) interactions have homologous
TFs sharing RG or homologous RGs sharing TFs. This
suggests that duplication is a major mechanism for
network growth
710 out of the 1233 interactions have either TF with a
homologue or RG with a homologue but not share RG
or TF, suggesting innovation of new edges or
duplication followed by loss of regulatory interactions.
123 out of the 1233 interactions have no homologues
for TFs and RG suggesting that these interactions were
innovations.